Transcoder products have typically been limited to one or two channels. However, system-on-a-chip (“SOC”) technologies allow a transcoder product to integrate a larger number of transcoder channels into a single chassis via multiple transcoder SOC instances. The transcoder SOC instances may perform transcoding in parallel. A host central processor unit (“CPU”) communicates with each of the transcoder SOC instances to coordinate the transcoding. When using multiple transcoder instances, unless the transcoders are initialized or synchronized to begin transcoding at the same time, there may be a time delay or gap in information (e.g., misaligned segments) from one transcoder to another. This may cause problems for streaming video, such as when changing from one resolution or compression rate to another if the segments from one compression rate do not align with the segments from another compression rate. This not-so-seamless transition is undesirable for viewers and should be minimized or eliminated.